OK - we will need a bit *more* information. I see you are using Mach4 build 2230. What PMDX-SmartBOB plugin version and firmware version are you running? To get this info, go to the "Configure" menu and select "Plugins...", then click on the "Configure" button next to the PMDX-SmartBOB-USB plugin. The first screen will list all of the relevant info.
Hmmmm.... Now that I look at your post again, a possible cause of this kind of problem is that you have the motor's max velocity set too high. By default, Mach4 sets the jogging speed to 50% of max velocity. You can see this when you click on the "Jogging" tab in the lower portion of the Mach4 screen set. There is a slider at the bottom and a "Jog Rate" box. Try setting the jog rate to 100% and see if jogging reproduces the same motion anomalies as GCode motion. If so, go to the "Configure" menu and select "Mach...", then click on the "Motors" tab and try setting the "Velocity" field to a lower value. If that doesn't fix things, then please post the above info.
Bob